Contacts of the strand formed by residues 401 - 410 (chain A) in PDB entry 2Q7N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A VAL* 4.0 22.4 - - + -
394A LYS 3.4 12.1 - - - +
395A ASP* 4.4 13.7 - - - +
396A ILE* 3.5 9.5 - - - +
400A VAL* 1.3 78.5 - - - +
402A THR* 1.3 59.9 + - - +
403A PHE* 5.4 0.7 - - + +
447A ALA 3.7 0.5 - - - -
448A VAL* 2.8 64.8 + - + +
451A LEU* 4.3 13.0 - - + -
459A PHE* 4.4 13.7 - - + -
480A HIS* 4.6 4.9 - - - +
482A THR* 4.7 12.3 - - + -
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Residues in contact with THR 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LYS 3.6 2.1 - - - +
393A VAL* 3.4 6.6 - - - -
394A LYS* 2.6 49.8 + - + -
396A ILE* 3.6 17.6 - - - +
401A VAL* 1.3 69.9 + - - +
403A PHE* 1.3 57.9 + - - +
404A SER* 3.7 14.9 + - - +
445A HIS* 5.1 11.3 - - + +
446A VAL 3.5 8.6 + - - +
447A ALA* 4.7 4.7 - - - +
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Residues in contact with PHE 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A LEU* 3.5 28.7 - - + -
392A LYS 3.9 2.7 - - - -
393A VAL* 3.6 21.3 - - + -
401A VAL* 3.7 1.9 + - + -
402A THR* 1.3 70.8 - - - +
404A SER* 1.3 58.3 + - - +
405A TRP* 3.2 27.0 - + - -
420A ILE* 3.3 18.2 - - + -
446A VAL* 2.7 47.1 + - - +
448A VAL* 4.0 17.3 - - + -
459A PHE* 3.0 39.7 - + + -
460A ARG 4.2 4.5 - - - -
461A VAL* 3.1 33.0 - - + -
478A LYS* 3.8 11.0 - - + -
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A SER 4.0 0.2 - - - +
391A LEU* 3.3 6.1 - - - +
392A LYS* 2.9 50.3 + - - +
394A LYS* 5.8 0.3 - - - +
402A THR* 3.7 12.4 + - - +
403A PHE* 1.3 78.0 - - - +
405A TRP* 1.3 66.2 + - - +
443A THR* 5.9 1.1 - - - -
444A TYR 3.1 5.4 - - - -
445A HIS* 3.3 33.7 - - - -
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Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A PRO* 3.7 18.6 - - + -
389A THR 3.5 8.1 - - - +
390A SER 4.2 5.4 - - - -
391A LEU* 3.4 25.6 - - + -
403A PHE* 3.2 48.2 - + - -
404A SER* 1.3 78.8 - - - +
406A TYR* 1.3 78.6 + - - +
407A LEU* 4.2 5.1 - - + +
418A CYS* 4.0 22.9 - - + -
420A ILE* 4.6 2.5 - - + -
436A ILE* 4.6 3.6 - - + -
443A THR* 2.9 32.2 - - - +
444A TYR* 2.9 38.3 + + + +
446A VAL* 3.6 23.8 - - + -
461A VAL* 3.7 19.3 - - + -
463A CYS* 3.9 13.9 - - - -
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Residues in contact with TYR 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A THR* 3.1 32.4 + - - +
390A SER* 5.3 7.6 - - - +
405A TRP* 1.3 81.6 - - - +
407A LEU* 1.3 67.4 + - - +
408A PRO* 3.6 36.9 - - + +
441A ASP* 4.0 28.2 + - - +
442A SER 3.9 6.3 - - - -
443A THR* 3.9 21.3 - - + -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A PRO* 4.0 15.0 - - + -
386A HIS* 3.9 27.6 - - + +
388A PRO* 4.5 9.4 - - + -
405A TRP* 4.2 10.1 - - + +
406A TYR* 1.3 78.6 - - - +
408A PRO* 1.3 86.2 - - + +
409A GLY 3.7 2.1 + - - +
411A PHE* 4.5 9.0 - - + -
416A LEU* 3.9 20.4 - - + -
441A ASP* 4.1 0.2 - - - -
442A SER 3.5 23.4 + - - +
444A TYR* 4.0 14.0 + - + -
463A CYS* 3.7 37.5 - - + -
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Residues in contact with PRO 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A HIS 4.4 3.3 - - - +
297A ASP* 5.3 0.9 - - + -
386A HIS* 3.7 31.6 + - + +
387A ASP 4.8 8.1 - - - +
389A THR* 5.1 2.9 - - - +
406A TYR* 3.6 30.0 - - + +
407A LEU* 1.3 99.0 - - + +
409A GLY* 1.3 56.8 + - - +
411A PHE* 3.3 14.2 - - - -
441A ASP* 3.7 10.1 - - - +
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Residues in contact with GLY 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ASP* 4.2 20.4 - - - +
299A LYS* 5.3 1.6 - - - -
407A LEU 3.7 0.9 + - - +
408A PRO* 1.3 72.3 - - - +
410A ASN* 1.3 60.4 + - - -
411A PHE* 3.0 17.4 - - - -
439A ALA 3.0 19.4 - - - +
441A ASP* 2.9 27.1 + - - -
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A LEU* 3.2 46.5 + - + +
299A LYS* 4.9 12.9 - - + +
353A PRO* 5.8 0.8 - - - +
409A GLY* 1.3 67.4 - - - -
411A PHE* 1.3 62.5 + - - +
412A THR* 2.9 21.3 + - - -
439A ALA 4.2 1.3 - - - -
440A GLU* 3.8 20.2 - - + +
441A ASP* 4.6 0.2 + - - -
1L NAG 1.4 70.2 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il